Execute file remotely via FTP

I need to execute a batch file which will execute another application remotely via ftp. I have a server which supports the SITE EXEC command (which allows me to execute programs remotely). I can use this command to execute batch files which then execute other programs, but the problem I have lies in the fact that my ftp server starts as a system process.

Normally, when you locally execute a batch file that in turn starts 1 or more programs, the batch file not being a system process but rather a process for a specific user, starts the program(s) as specific user processes, for the same user that executed the batch file.

I want to have the program i want start for a specific user, executed remotely, but i can't do that now, since all programs executed remotely end up being a system process.

For example (a rather bad example), I can start edonkey as a system process remotely via ftp from school if i forget to turn it on before i leave, but this means that when I get home, I can't work with the program since its a system process, started by a batch file executed by a system process (ftp server).

Is there any solution to my predicament so I can execute remotely so programs start as a process for a specific user using the file transfer protocol? Right now, all I can do successfully is print jobs w/ notepad because i know the command line and it doesn't matter if its a system process. Is there some batch file command that specifically starts a program as a process for a specific user?